Gene detail

Detailed information of OS493_016275-T1 in Lophelia pertusa

Genomic Location: scaffold_49:2387380...2390570
NR annotation: KAJ7391968.1, Peptide methionine sulfoxide reductase B2, chloroplastic [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
B1J4W5	Peptide methionine sulfoxide reductase MsrB OS=Pseudomonas putida (strain W619) OX=390235 GN=msrB PE=3 SV=1
Q885Q1	Peptide methionine sulfoxide reductase MsrB OS=Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000) OX=223283 GN=msrB PE=3 SV=1
Q4ZQC6	Peptide methionine sulfoxide reductase MsrB OS=Pseudomonas syringae pv. syringae (strain B728a) OX=205918 GN=msrB PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001881 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01641 all species →	SelR	SelR domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002579 all species →	Domain	Peptide methionine sulphoxide reductase MrsB domain	Interproscan
IPR028427 all species →	Family	Peptide methionine sulfoxide reductase MsrB	Interproscan
IPR011057 all species →	Homologous_superfamily	Mss4-like superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10173 all species →	METHIONINE SULFOXIDE REDUCTASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0033743 all species →	Molecular Function	peptide-methionine (R)-S-oxide reductase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006979 all species →	Biological Process	response to oxidative stress	Interproscan
GO:0016671 all species →	Molecular Function	oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor	Interproscan
GO:0030091 all species →	Biological Process	protein repair	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K07305	msrB; peptide-methionine (R)-S-oxide reductase	EC:1.8.4.12	Enzymes with EC numbers	-	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_016275-T1 across 110 RNA-seq samples of Lophelia pertusa. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

110Samples

89TPM > 0

7Conditions

10.0Max TPM

2.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	11	1.65	4.56
polyp at pH7 6	18	8	1.36	6.46
coral polyp · control treatment	16	16	2.90	5.77
coral polyp · oil and dispersant treatment	16	16	2.23	9.16
coral polyp · oil treatment	16	15	2.49	5.11
coral polyp · dispersant treatment	16	13	1.10	4.55
Polyp	10	10	4.94	10.03

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.56
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.13
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.26
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.11
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.83
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.40
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.39
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.91
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.91
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.70
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.48
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.46
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.96
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.81
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.66
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.62
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.58
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.25
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.09
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.77
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.65
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.02
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.01
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.55
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.33
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.07
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.72
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.57
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.44
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.06
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.35
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.30
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.27
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.14
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.11
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.16
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.02
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.38
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.03
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.70
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.67
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.56
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.53
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.46
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.45
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.36
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.30
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.14
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.09
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.95
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.90
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.11
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.54
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.35
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.27
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.19
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.18
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.17
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.63
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.61
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.95
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.91
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.70
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.66
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.60
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.04
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.55
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.19
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.11
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.84
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.40
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.30
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.05
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.75
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.70
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.67
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.57
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.23
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.19
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	10.03
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	7.43
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.05
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	5.90
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.34
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.56
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.49
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.39
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.33
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.88

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.